Create VAF corplots of tumors across multiple timepoints for thr autopsy samples in the PBTA Cohort

Tumor evolution project

Data used

In this notebook, we are using the maf_autopsy.tsv file generated from the 01-preprocess-data.Rmd script. We will also use the oncoprint goi list from OpenPedCan oncoprint-goi-lists-OpenPedCan-gencode-v39.csv.

Set up

suppressPackageStartupMessages({
  library(tidyverse)
  library(ggrepel)
})

Directories and File Inputs/Outputs

# Detect the ".git" folder. This will be in the project root directory.
# Use this as the root directory to ensure proper sourcing of functions
# no matter where this is called from.
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
scratch_dir <- file.path(root_dir, "scratch")
analysis_dir <- file.path(root_dir, "analyses", "tmb-vaf-longitudinal") 
input_dir <- file.path(analysis_dir, "input")

# Input files
maf_autopsy_file <- file.path(scratch_dir, "maf_autopsy.tsv")
oncoprint_goi_file <- file.path(input_dir, "oncoprint-goi-lists-OpenPedCan-gencode-v39.csv")
timepoint_color_palette_file <- file.path(root_dir, "figures", "palettes", "timepoint_color_palette.tsv")

# File path to plots directory
plots_dir <-
  file.path(analysis_dir, "plots")
if (!dir.exists(plots_dir)) {
  dir.create(plots_dir)
}

source(paste0(analysis_dir, "/util/function-create-corplot.R"))
source(paste0(root_dir, "/figures/scripts/theme.R"))

Read in data and process

# Read maf_autopsy file generated from step `01-process-data.Rmd`
maf_autopsy <- readr::read_tsv(maf_autopsy_file, guess_max = 100000, show_col_types = FALSE)

# Read oncoprint_goi_file
# We will use the following list of genes and then we will create a label to select the ones for the corplots.
oncoprint_goi <- read.csv(oncoprint_goi_file, stringsAsFactor = FALSE) %>%
  select(LGAT, Embryonal.tumor, HGAT, Other) 

# let's create a list with the genes to be used for the corplots
oncoprint_goi <- data.frame(goi_list = unlist(oncoprint_goi)) 

# remove empty rows
oncoprint_goi <- oncoprint_goi[!apply(oncoprint_goi == "", 1, all), ] 
oncoprint_goi <- data.frame(oncoprint_goi)

# Read timepoint_color_palette file
timepoint_color_palette <- readr::read_tsv(timepoint_color_palette_file, guess_max = 100000, show_col_types = FALSE)

Corplots for each Patient case and per biospecimen_id and timepoint

# We will define samples based on the "Kids_First_Participant_ID" column 
samples <- unique(as.character(maf_autopsy$Kids_First_Participant_ID))
print(samples)

 [1] "PT_19GCSK2S" "PT_1H2REHT2" "PT_23NZGSRJ" "PT_37B5JRP1" "PT_394ZA6P7" "PT_3CHB9PK5"
 [7] "PT_3KM9W8S8" "PT_5NS35B66" "PT_6N825561" "PT_75HRTX4S" "PT_8GN3TQRM" "PT_CXT81GRM"
[13] "PT_DNAJYFZT" "PT_DVXE38EX" "PT_FA2F3HQG" "PT_GTHZF21E" "PT_HFQNKP5X" "PT_HJMP6PH2"
[19] "PT_KBFM551M" "PT_KTRJ8TFY" "PT_KZ56XHJT" "PT_MDWPRDBT" "PT_MNSEJCDM" "PT_NJQ26FHN"
[25] "PT_NZ85YSJ1" "PT_PR4YBBH3" "PT_RJ1TJ2KH" "PT_WYXTEG3E" "PT_Z4BF2NSB"

for (i in seq_along(samples)) {
  print(i)
  maf_sub <- maf_autopsy %>%
    filter(Kids_First_Participant_ID == samples[i])
  timepoints_other_plots <- unique(maf_sub$timepoints_other)
  timepoints_other_plots <- timepoints_other_plots[!timepoints_other_plots == "4"]
  print(timepoints_other_plots)
  timepoints_deceased_plots <- unique(maf_sub$timepoints_deceased)
  timepoints_deceased_plots <- timepoints_deceased_plots[!timepoints_deceased_plots %in% c("1", "2", "3")]
  print(timepoints_deceased_plots)
  
# Run corplot
  for (t in seq_along(timepoints_deceased_plots)){
    for (k in seq_along(timepoints_other_plots)){
      fname <- paste0(plots_dir, "/", samples[i], "-", timepoints_other_plots[k], "-vs-", timepoints_deceased_plots[t], "-vaf-corplot.pdf")
      print(fname)
      p <- create_corplot(maf = maf_sub,
                          timepoints_other_plot = timepoints_other_plots[k],
                          timepoints_deceased_plot = timepoints_deceased_plots[t],
                          sid = samples[i])
      pdf(file = fname, width = 10, height = 8)
      print(p)
      dev.off()
    }
  }
  }  

[1] 1
[1] "Diagnosis_BS_3KD309X6"
[1] "Deceased_BS_AH252MTC" "Deceased_BS_FZ8D57HJ" "Deceased_BS_GH6PH611"
[4] "Deceased_BS_NXT37ZPA"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_AH252MTC-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_FZ8D57HJ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_GH6PH611-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_19GCSK2S-Diagnosis_BS_3KD309X6-vs-Deceased_BS_NXT37ZPA-vaf-corplot.pdf"
[1] 2
[1] "Progressive_BS_79SYEHY3" "Progressive_BS_7M7JNG00"
[1] "Deceased_BS_96S0VQBN"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_1H2REHT2-Progressive_BS_79SYEHY3-vs-Deceased_BS_96S0VQBN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_1H2REHT2-Progressive_BS_7M7JNG00-vs-Deceased_BS_96S0VQBN-vaf-corplot.pdf"
[1] 3
[1] "Diagnosis_BS_05S9WJW6"
[1] "Deceased_BS_209RV8H2" "Deceased_BS_CCHHH752" "Deceased_BS_CJ2G78ZZ"
[4] "Deceased_BS_F2MTFYFR" "Deceased_BS_GNXGGWFN" "Deceased_BS_H8JZ6CZR"
[7] "Deceased_BS_Q03MVGN6"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_209RV8H2-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_CCHHH752-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_CJ2G78ZZ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_F2MTFYFR-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_GNXGGWFN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_H8JZ6CZR-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_23NZGSRJ-Diagnosis_BS_05S9WJW6-vs-Deceased_BS_Q03MVGN6-vaf-corplot.pdf"
[1] 4
[1] "Diagnosis_BS_EJV0N3BX"
[1] "Deceased_BS_8Q8N6AHW"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_37B5JRP1-Diagnosis_BS_EJV0N3BX-vs-Deceased_BS_8Q8N6AHW-vaf-corplot.pdf"
[1] 5
[1] "Diagnosis_BS_1KP6JADZ"
[1] "Deceased_BS_Q41J76W9"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_394ZA6P7-Diagnosis_BS_1KP6JADZ-vs-Deceased_BS_Q41J76W9-vaf-corplot.pdf"
[1] 6
[1] "Diagnosis_BS_20TBZG09"
[1] "Deceased_BS_8AY2GM4G"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_3CHB9PK5-Diagnosis_BS_20TBZG09-vs-Deceased_BS_8AY2GM4G-vaf-corplot.pdf"
[1] 7
[1] "Diagnosis_BS_859AV1DB"
[1] "Deceased_BS_2NQXY528" "Deceased_BS_4BB136DY" "Deceased_BS_EQQZ90JQ"
[4] "Deceased_BS_MS8TBCWJ" "Deceased_BS_P8FXRTZ2" "Deceased_BS_QR84QJN4"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_2NQXY528-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_4BB136DY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_EQQZ90JQ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_MS8TBCWJ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_P8FXRTZ2-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_3KM9W8S8-Diagnosis_BS_859AV1DB-vs-Deceased_BS_QR84QJN4-vaf-corplot.pdf"
[1] 8
[1] "Diagnosis_BS_SVKMG97S"
[1] "Deceased_BS_F0JN3TFM"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_5NS35B66-Diagnosis_BS_SVKMG97S-vs-Deceased_BS_F0JN3TFM-vaf-corplot.pdf"
[1] 9
[1] "Progressive_BS_E0S2Y0TS"
[1] "Deceased_BS_0YWFFRYV" "Deceased_BS_3V7ZNBTG" "Deceased_BS_YTCYVVY9"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_0YWFFRYV-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_3V7ZNBTG-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_6N825561-Progressive_BS_E0S2Y0TS-vs-Deceased_BS_YTCYVVY9-vaf-corplot.pdf"
[1] 10
[1] "Diagnosis_BS_7YGM7F5R"
[1] "Deceased_BS_3CDQYJ5Q" "Deceased_BS_WTGPN218"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_75HRTX4S-Diagnosis_BS_7YGM7F5R-vs-Deceased_BS_3CDQYJ5Q-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_75HRTX4S-Diagnosis_BS_7YGM7F5R-vs-Deceased_BS_WTGPN218-vaf-corplot.pdf"
[1] 11
[1] "Recurrence_BS_QQP17PDQ"  "Progressive_BS_RXSBJ929"
[1] "Deceased_BS_S791VC80"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_8GN3TQRM-Recurrence_BS_QQP17PDQ-vs-Deceased_BS_S791VC80-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_8GN3TQRM-Progressive_BS_RXSBJ929-vs-Deceased_BS_S791VC80-vaf-corplot.pdf"
[1] 12
[1] "Diagnosis_BS_HZNKSQ17"
[1] "Deceased_BS_3CG2N4PD"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_CXT81GRM-Diagnosis_BS_HZNKSQ17-vs-Deceased_BS_3CG2N4PD-vaf-corplot.pdf"
[1] 13
[1] "Recurrence_BS_EJ1H9PZY"
[1] "Deceased_BS_8XJJVBQP"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_DNAJYFZT-Recurrence_BS_EJ1H9PZY-vs-Deceased_BS_8XJJVBQP-vaf-corplot.pdf"
[1] 14
[1] "Diagnosis_BS_NSWP72M6"   "Progressive_BS_P3R9QZKP" "Recurrence_BS_Y386XSV3" 
[1] "Deceased_BS_ERRA7V0W"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_DVXE38EX-Diagnosis_BS_NSWP72M6-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_DVXE38EX-Progressive_BS_P3R9QZKP-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_DVXE38EX-Recurrence_BS_Y386XSV3-vs-Deceased_BS_ERRA7V0W-vaf-corplot.pdf"
[1] 15
[1] "Diagnosis_BS_G9WRA2N1"
[1] "Deceased_BS_S78482NX"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_FA2F3HQG-Diagnosis_BS_G9WRA2N1-vs-Deceased_BS_S78482NX-vaf-corplot.pdf"
[1] 16
[1] "Diagnosis_BS_N4S9T8F5"
[1] "Deceased_BS_3A7YMV93" "Deceased_BS_5PR4KXE1" "Deceased_BS_D3BH8D4Y"
[4] "Deceased_BS_EV071CE1" "Deceased_BS_FQBVBTCY" "Deceased_BS_M4KR9DSE"
[7] "Deceased_BS_T3WNX1E2" "Deceased_BS_Z7806Z75"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_3A7YMV93-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_5PR4KXE1-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_D3BH8D4Y-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_EV071CE1-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_FQBVBTCY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_M4KR9DSE-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_T3WNX1E2-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_GTHZF21E-Diagnosis_BS_N4S9T8F5-vs-Deceased_BS_Z7806Z75-vaf-corplot.pdf"
[1] 17
[1] "Recurrence_BS_6F49F7WH"  "Progressive_BS_9GN1QA3Q" "Progressive_BS_FBJ516WW"
[1] "Deceased_BS_2MPNPD28" "Deceased_BS_5B6XZ7YP" "Deceased_BS_FVPZ3CYY"
[4] "Deceased_BS_MAHWW7NR" "Deceased_BS_SCW1FS55" "Deceased_BS_VZB4K7NV"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_2MPNPD28-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_5B6XZ7YP-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_FVPZ3CYY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_MAHWW7NR-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_SCW1FS55-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Recurrence_BS_6F49F7WH-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_9GN1QA3Q-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HFQNKP5X-Progressive_BS_FBJ516WW-vs-Deceased_BS_VZB4K7NV-vaf-corplot.pdf"
[1] 18
[1] "Recurrence_BS_9SVMVJ45" "Diagnosis_BS_XKM2EAT4" 
[1] "Deceased_BS_3XW15QAZ" "Deceased_BS_4CT3A9PQ" "Deceased_BS_FS48BMA3"
[4] "Deceased_BS_GXFX6VW1" "Deceased_BS_RNAADGMF"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_3XW15QAZ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_3XW15QAZ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_4CT3A9PQ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_4CT3A9PQ-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_FS48BMA3-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_FS48BMA3-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_GXFX6VW1-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_GXFX6VW1-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HJMP6PH2-Recurrence_BS_9SVMVJ45-vs-Deceased_BS_RNAADGMF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_HJMP6PH2-Diagnosis_BS_XKM2EAT4-vs-Deceased_BS_RNAADGMF-vaf-corplot.pdf"
[1] 19
[1] "Diagnosis_BS_9P4NDTKJ" "Diagnosis_BS_M0B42FPR" "Diagnosis_BS_M5FM63EB"
[4] "Diagnosis_BS_WYTDVC0Y"
[1] "Deceased_BS_J8EK6RNF"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KBFM551M-Diagnosis_BS_9P4NDTKJ-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KBFM551M-Diagnosis_BS_M0B42FPR-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KBFM551M-Diagnosis_BS_M5FM63EB-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KBFM551M-Diagnosis_BS_WYTDVC0Y-vs-Deceased_BS_J8EK6RNF-vaf-corplot.pdf"
[1] 20
[1] "Diagnosis_BS_3VKW5988" "Diagnosis_BS_402W79TS" "Diagnosis_BS_BQ81D2BP"
[1] "Deceased_BS_5968GBGT" "Deceased_BS_AF5D41PD" "Deceased_BS_EE73VE7V"
[4] "Deceased_BS_HYKV2TH9"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_5968GBGT-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_AF5D41PD-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_EE73VE7V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_3VKW5988-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_402W79TS-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KTRJ8TFY-Diagnosis_BS_BQ81D2BP-vs-Deceased_BS_HYKV2TH9-vaf-corplot.pdf"
[1] 21
[1] "Progressive_BS_0ATJ22QA" "Progressive_BS_9DN4QR6E" "Diagnosis_BS_FWP8ZA4K"  
[4] "Diagnosis_BS_H8NWA41N"  
[1] "Deceased_BS_1Q524P3B" "Deceased_BS_22VCR7DF" "Deceased_BS_AK9BV52G"
[4] "Deceased_BS_D6STCMQS" "Deceased_BS_X5VN0FW0" "Deceased_BS_YHXMYDBN"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_1Q524P3B-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_22VCR7DF-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_AK9BV52G-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_D6STCMQS-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_X5VN0FW0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_0ATJ22QA-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Progressive_BS_9DN4QR6E-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_FWP8ZA4K-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_KZ56XHJT-Diagnosis_BS_H8NWA41N-vs-Deceased_BS_YHXMYDBN-vaf-corplot.pdf"
[1] 22
[1] "Recurrence_BS_00TRPEQX"  "Recurrence_BS_BQWMQM2Y"  "Progressive_BS_D368BNRD"
[1] "Deceased_BS_1M63B97V"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_MDWPRDBT-Recurrence_BS_00TRPEQX-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_MDWPRDBT-Recurrence_BS_BQWMQM2Y-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_MDWPRDBT-Progressive_BS_D368BNRD-vs-Deceased_BS_1M63B97V-vaf-corplot.pdf"
[1] 23
[1] "Diagnosis_BS_CBMAWSAR" "Diagnosis_BS_ZSH09N84"
[1] "Deceased_BS_J8EH1N7V" "Deceased_BS_Y74XAFJX"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_MNSEJCDM-Diagnosis_BS_CBMAWSAR-vs-Deceased_BS_J8EH1N7V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_MNSEJCDM-Diagnosis_BS_ZSH09N84-vs-Deceased_BS_J8EH1N7V-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_MNSEJCDM-Diagnosis_BS_CBMAWSAR-vs-Deceased_BS_Y74XAFJX-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_MNSEJCDM-Diagnosis_BS_ZSH09N84-vs-Deceased_BS_Y74XAFJX-vaf-corplot.pdf"
[1] 24
[1] "Recurrence_BS_JZ61AA7Z" "Diagnosis_BS_NXTB7A9N" 
[1] "Deceased_BS_7XEEQM3X" "Deceased_BS_AYR6PJN0"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_NJQ26FHN-Recurrence_BS_JZ61AA7Z-vs-Deceased_BS_7XEEQM3X-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_NJQ26FHN-Diagnosis_BS_NXTB7A9N-vs-Deceased_BS_7XEEQM3X-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_NJQ26FHN-Recurrence_BS_JZ61AA7Z-vs-Deceased_BS_AYR6PJN0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_NJQ26FHN-Diagnosis_BS_NXTB7A9N-vs-Deceased_BS_AYR6PJN0-vaf-corplot.pdf"
[1] 25
[1] "Diagnosis_BS_4HRYS7JY"
[1] "Deceased_BS_Q7QH96SX"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_NZ85YSJ1-Diagnosis_BS_4HRYS7JY-vs-Deceased_BS_Q7QH96SX-vaf-corplot.pdf"
[1] 26
[1] "Diagnosis_BS_PPY0EWPG"
[1] "Deceased_BS_C2NH5FDT"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_PR4YBBH3-Diagnosis_BS_PPY0EWPG-vs-Deceased_BS_C2NH5FDT-vaf-corplot.pdf"
[1] 27
[1] "Diagnosis_BS_6GN1FGTB"
[1] "Deceased_BS_6VKKMM6M"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_RJ1TJ2KH-Diagnosis_BS_6GN1FGTB-vs-Deceased_BS_6VKKMM6M-vaf-corplot.pdf"
[1] 28
[1] "Progressive_BS_G9B420R9"
[1] "Deceased_BS_H13TBC1X"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_WYXTEG3E-Progressive_BS_G9B420R9-vs-Deceased_BS_H13TBC1X-vaf-corplot.pdf"
[1] 29
[1] "Recurrence_BS_EJP43CD9" "Diagnosis_BS_W2QCHQ7E" 
[1] "Deceased_BS_2T4EJ6KN" "Deceased_BS_537YFJ06" "Deceased_BS_C6T8F9K7"
[4] "Deceased_BS_GSXNQNRY" "Deceased_BS_M29BNE7Z" "Deceased_BS_MRN9VDQ0"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_2T4EJ6KN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_2T4EJ6KN-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_537YFJ06-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_537YFJ06-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_C6T8F9K7-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_C6T8F9K7-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_GSXNQNRY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_GSXNQNRY-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_M29BNE7Z-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_M29BNE7Z-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Recurrence_BS_EJP43CD9-vs-Deceased_BS_MRN9VDQ0-vaf-corplot.pdf"
[1] "/Users/chronia/CHOP/GitHub/pbta-tumor-evolution/analyses/tmb-vaf-longitudinal/plots/PT_Z4BF2NSB-Diagnosis_BS_W2QCHQ7E-vs-Deceased_BS_MRN9VDQ0-vaf-corplot.pdf"

sessionInfo()

R version 4.2.3 (2023-03-15)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggthemes_4.2.4  ggrepel_0.9.3   flextable_0.9.2 lubridate_1.9.2 forcats_1.0.0  
 [6] stringr_1.5.0   dplyr_1.1.2     purrr_1.0.1     readr_2.1.4     tidyr_1.3.0    
[11] tibble_3.2.1    ggplot2_3.4.2   tidyverse_2.0.0

loaded via a namespace (and not attached):
 [1] sass_0.4.7              pkgload_1.3.2.1         bit64_4.0.5            
 [4] vroom_1.6.3             jsonlite_1.8.7          R.utils_2.12.2         
 [7] bslib_0.5.0             shiny_1.7.4.1           askpass_1.1            
[10] fontLiberation_0.1.0    yaml_2.3.7              gdtools_0.3.3          
[13] pillar_1.9.0            glue_1.6.2              uuid_1.1-0             
[16] digest_0.6.33           promises_1.2.0.1        colorspace_2.1-0       
[19] htmltools_0.5.5         httpuv_1.6.11           R.oo_1.25.0            
[22] gfonts_0.2.0            fontBitstreamVera_0.1.1 pkgconfig_2.0.3        
[25] httpcode_0.3.0          xtable_1.8-4            scales_1.2.1           
[28] later_1.3.1             officer_0.6.2           fontquiver_0.2.1       
[31] tzdb_0.4.0              timechange_0.2.0        openssl_2.1.0          
[34] farver_2.1.1            generics_0.1.3          ellipsis_0.3.2         
[37] cachem_1.0.8            withr_2.5.0             cli_3.6.1              
[40] magrittr_2.0.3          crayon_1.5.2            mime_0.12              
[43] evaluate_0.21           R.methodsS3_1.8.2       fansi_1.0.4            
[46] xml2_1.3.5              textshaping_0.3.6       tools_4.2.3            
[49] data.table_1.14.8       hms_1.1.3               lifecycle_1.0.3        
[52] munsell_0.5.0           zip_2.3.0               compiler_4.2.3         
[55] jquerylib_0.1.4         systemfonts_1.0.4       rlang_1.1.1            
[58] rstudioapi_0.15.0       labeling_0.4.2          rmarkdown_2.23         
[61] gtable_0.3.3            curl_5.0.1              R6_2.5.1               
[64] knitr_1.43              fastmap_1.1.1           bit_4.0.5              
[67] utf8_1.2.3              rprojroot_2.0.3         ragg_1.2.5             
[70] stringi_1.7.12          parallel_4.2.3          crul_1.4.0             
[73] Rcpp_1.0.11             vctrs_0.6.3             tidyselect_1.2.0       
[76] xfun_0.39